# ========= [INFO] ==========
# Mut inCB: not accepter mutation in BC
# Mut inMS: 2
# ReadIn  : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam
# seq_deb : TCAGGTG
# seq_fin : CGTGG
# MS_seq : AT
# excl : C,G
# nom  : AT20
# =============================
#
#-------------- Filt ------------------
# condiGrep: TCAG.TG[ATCGN]+ATATATATAT[ATCGN]+.GTGG|TCAG.TG[ATCGN]+ATATATATAT[ATCGN]+C.TGG|TCAG.TG[ATCGN]+ATATATATAT[ATCGN]+CG.GG|TCAG.TG[ATCGN]+ATATATATAT[ATCGN]+CGT.G|TCAG.TG[ATCGN]+ATATATATAT[ATCGN]+CGTG.|TCAGG.G[ATCGN]+ATATATATAT[ATCGN]+.GTGG|TCAGG.G[ATCGN]+ATATATATAT[ATCGN]+C.TGG|TCAGG.G[ATCGN]+ATATATATAT[ATCGN]+CG.GG|TCAGG.G[ATCGN]+ATATATATAT[ATCGN]+CGT.G|TCAGG.G[ATCGN]+ATATATATAT[ATCGN]+CGTG.|TCAGGT.[ATCGN]+ATATATATAT[ATCGN]+.GTGG|TCAGGT.[ATCGN]+ATATATATAT[ATCGN]+C.TGG|TCAGGT.[ATCGN]+ATATATATAT[ATCGN]+CG.GG|TCAGGT.[ATCGN]+ATATATATAT[ATCGN]+CGT.G|TCAGGT.[ATCGN]+ATATATATAT[ATCGN]+CGTG.
# condiGrep Rev-Compt: .CACG[NCGAT]+ATATATATAT[NCGAT]+.ACCTGA|C.ACG[NCGAT]+ATATATATAT[NCGAT]+.ACCTGA|CC.CG[NCGAT]+ATATATATAT[NCGAT]+.ACCTGA|CCA.G[NCGAT]+ATATATATAT[NCGAT]+.ACCTGA|CCAC.[NCGAT]+ATATATATAT[NCGAT]+.ACCTGA|.CACG[NCGAT]+ATATATATAT[NCGAT]+C.CCTGA|C.ACG[NCGAT]+ATATATATAT[NCGAT]+C.CCTGA|CC.CG[NCGAT]+ATATATATAT[NCGAT]+C.CCTGA|CCA.G[NCGAT]+ATATATATAT[NCGAT]+C.CCTGA|CCAC.[NCGAT]+ATATATATAT[NCGAT]+C.CCTGA|.CACG[NCGAT]+ATATATATAT[NCGAT]+CA.CTGA|C.ACG[NCGAT]+ATATATATAT[NCGAT]+CA.CTGA|CC.CG[NCGAT]+ATATATATAT[NCGAT]+CA.CTGA|CCA.G[NCGAT]+ATATATATAT[NCGAT]+CA.CTGA|CCAC.[NCGAT]+ATATATATAT[NCGAT]+CA.CTGA
#--------------------------------------
module load picard/2.8.2
> java -jar /env/gfs/apps/picard/2.8.2/picard.jar SortSam I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.unmapped.sam O=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.unmapped.sort.sam SORT_ORDER=queryname 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.unmapped.bam ]
